Experiment / E6G85JETGEpisomal Plasmid MPRA

mNPC primeTF reporter stimulation and heat-shock panel

Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays

Fully differentiated mouse neural precursor cells were profiled with the episomal primeTF reporter library after heat shock or forskolin stimulation. The table covers 3 h heat shock and 4 h or 24 h forskolin conditions relative to untreated mNPCs.

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Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.

Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CL:0011020
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

43 C heat shock for 3 h or 10 uM forskolin for 4 h or 24 h in fully differentiated mNPCs.

The primeTF reporter plasmid library was transfected into fully differentiated mNPCs and reporter RNA barcodes were sequenced. PrimeTF activity was normalized to plasmid DNA and analyzed with primetime; paired chromVAR and TOBIAS values are included for comparison.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (14 of 14)

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Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 14 definitions

reporter_tf: Name of the synthetic reporter and assayed transcription factor
condition: Condition label from Dataset EV1
control_state: Untreated fully differentiated mNPC baseline
tested_state: mNPC stimulation or heat-shock condition represented by the row
primetime_log2_fc: PrimeTF reporter activity log2 fold change for tested versus untreated mNPCs
primetime_adjusted_p_value: Adjusted p-value supplied for the primeTF reporter activity comparison
primetime_significance: Source significance call: Upregulated, Downregulated, or NS
chromvar_difference: Difference in chromVAR TF-associated accessibility score for the paired ATAC-seq comparison
chromvar_adjusted_p_value: Adjusted p-value for the paired chromVAR comparison
chromvar_significance: Source chromVAR significance call
tobias_log2_fc: TOBIAS ATAC-seq TF activity log2 fold change
tobias_p_value: TOBIAS comparison p-value
tobias_significance: Source TOBIAS significance call
qc_status: Row-level package QC status; passed means primeTF effect and adjusted p-value were numeric

Quality control

The paper used primetime v1.0 quality checks for low plasmid-DNA bleedthrough, high barcode correlation, and high biological-replicate correlation. Processed rows were retained only when Dataset EV1 supplied numeric primeTF log2 fold-change and adjusted p-value values; all 294 retained rows passed this package's numeric-value filter. NS is a statistical call, not a QC failure.

Curation notes

The publication reports mNPC heat shock and forskolin at 4 h and 24 h. The BioStudies Dataset EV1 is the source for all three conditions; the repository's NPC_FK text output is a supplemental partial result and was retained raw but not used to replace the expanded source-data rows.

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